phylociraptor v0.9.13 hashes

Changes since last release:
ffdbaf5 bump version to 0.9.13
97206e1 Comment out debug related output in report
2a8fb86 Several small fixes for hash calculation
3bfc669 Remove and recalculate duplicated quartets before writting output files so that number specified by -n is correct
24a7aae Make both trees in conflict plot face to the right
ef81ee1 Display raxml tree with support values in the report
3c403c6 Add hashing to t2t pca. Small code cleanup
a5468b7 Add hashing support to heatmap plotting
1d360be Update gitignore
3e8e982 Fix naming of trees for conflict plots
9c54c67 Add hashing to plot-tree
a2dc1e4 Fix up get-lineage for hashing
e0cae81 Add hashing functionality to figure report
36f9b2d Remove more testing output from report
6a74f46 Fix two small problems with how trimmed alignments are represented in the report
8688b31 First set of changes to incorporate hashing into the HTML report. This should generally work now.
4a1a44d Reorganize how phylogeny results are stored in results
ca85109 parse-log.py can not run inside a container.
b2df5e0 Rename some rulefiles for clarity
ae5f42a Fix some additional small problems with check and make yaml parameter files have a uniform prefix (parameters)
facde3f Fix small error in check for njtree
6ef125c Modify phylociraptor check to take into account analysis hashes. Also support hashes in initial checks for different runmodes.
327b646 Move hash functionality functions into libphylociraptor to be able to reuse them in check and other modules
758327e Change modify-busco script so that it creates new directories for each modified busco set instead of overwriting the original directory.
b817be9 Fix parsing of full busco table for busco 3
9c098f7 Fix hash calculation if no mode column is specified
39bb602 Fix error when no exclude files is specified or the file does not exist
3e5224d move function to make more general, control ruleorder
a18f4fd modeltest - add checkpoints from previous stage as input and control rule order
80a31cc add checkpoints from previous stage as input and control rule order
3c34773 add checkpoints from previous stage as input
d6c298b add checkpoint from previous stage as input
c5c5f6f make sure file is only read if it's there; move get_modeltest_checkpoint function to here
e5bb77a use rsync instead
8651061 Treat nodes without support values as unsupported in plot tree. Fixes #27
be9dc46 Small fixes to phylociraptor script.
eb8927a update fix aa also in second create_sequence_files occasion
52f8a2a hash functionality for speciestree section
58e6e9e hash functionality for njtree section
5a33252 hash functionality for mltree section
781cc5d hash functionality for modeltest section
6927b18 hash functionality for filter-align section
740e609 hash functionality for align section
420e00f hash functionality for filter-orthology section
3ff4e2d hash functionality for orthology section
ad48b8f config template update to structure used in hash branch
b78142e new script for reading and writing of yaml paramter files
5c68f38 add hash functions to functions.smk
8f0f843 export name of config file as environmental variable
322c3d2 add functions for hash functionality
6da485e update setup to new config file structure
47c95bd updated structure of config file
63196cf remove unneccesary outputs from raxml rule
3e1f6ab replace the rare aminoacid 'U' with 'X' since raxml can't handle
85e9a4b Fix small issue in how util plot-heatmap is called
44e32ce Capture additional R console output in plot scripts
4a54043 Fix bug in check related to new --verbose and --debug
5681db1 Improve behavior of --verbose and --debug.
dd200d2 Change behavior of phylociraptor --verbose. Now only a reduced set of the whole output is given, use --debug to see all output
0145064 Run parse-log.py inside a container to prevent python problems
6d9f7a6 Fix small error in how finished raxml trees are identified in check.
d5ada65 Add possibility to plot only a single uncollapsed tree and plot title and additional information to util plot-tree.
c227474 Fix error when trees for plot-conflict are not provided in correct order
1681241 Change colors in plot-conflict plots with no lineage info to match plots with lineage info.
9dcc16b Much improved plot-conflict utility: More information, colors instead of line thickness, better script output.
5fd8af4 Add possibility to provide a list of tips to estimate-conflict
b2aaf6a Separate plot-tree and plot-conflict scripts